Figure 4.7 highlights two other kinds of bonds. Note the decrease in the size of the Li atom (and the large positive charge) compared to the Li atom in Li–H. LiH is best thought of as Li+H- (i.e., the bonding electron pair belongs to H- rather than being shared), which is an example of ionic bonding.

Here is an interactive version of Figure 4.7a where the atomic densities of H and Li are superimposed on the density of H-Li.

Click on the picture for an interactive version

Li2 is more polar than H2: more positive at the ends and more negative in the middle, indicating the a larger rearrangement of electron density upon binding compared to H2. Here is an interactive version (the corresponding Jmol script can be found here; see this post on making plots like this), where I have superimposed the electron densities of the Li atoms and Li2:

Click on the picture for an interactive version

Looking deeper into the density (by using a larger, 0.01 au, isodensity value) reveals a density rearrangement that is quite different from H2:

Click on the picture for an interactive version

Here you can see strong localization of electron density between the nuclei, indicating that Li2 is best thought of as Li+:Li+, where ":" indicates an electron pair. This is an example of metallic bonding.

Both ionic and metallic bonding are distinctly different from covalent bonding, in that only covalent bonding leads to the formation of distinct molecules, while ionic and metallic bonding leads to formation of crystals.

Why do I use a different isodensity value for this plot?I usually use a 0.002 au isodensity surface, but in Figure 4.7 I use 0.0005. This is something I didn't discuss in the book but should have. When I made the plot of the 0.002 au isodensity surface with superimposed electrostatic potential of Li atom, I discovered that is was very blue, i.e. quite positive (go ahead, try it for yourself). I only got a neutral-looking atom when I went down to 0.0005 aus, which is what I have used for the figures (unless otherwise noted).

The positive electrostatic potential on the 0.002 au isodensity surface of Li indicates that a significant amount of density is found outside this surface, which is clearly not the case of the H atom, as shown in a previous post. This, in turn, indicates that the Li electron density decreases more slowly with distance compared to H, which makes sense since Li is much less electronegative than H. Thus, the 0.002 au isodensity surface is a reflection of the van der Waals surface of organic molecules (containing electronegative elements) but not alkali metals.

If we look at the electron density of H2 (Figure 4.5a), we can clearly see that at this separation the electron densities of the two H atoms have fused indicating electron sharing, a hallmark of covalent bonding. Here is an interactive version (the corresponding Jmol script can be found here; see this post on making plots like this), where I have superimposed the electron densities of the H atoms and H2:

Click on the picture for an interactive version

What you can't see in this picture is that the electron density has rearranged significantly between the nuclei, which is the source of the bond strength. To see this we need to look at a larger isodensity value (here 0.075 au):

Tuesday, February 16, 2010

Some exciting developments over at the Molecular Workbench (MW) blog run by MW author Charles Xie. I have several blog posts on MW, but it was necessary to install MW to check it out for yourself. Now it is possible to embed a MW applet in web pages (and blog posts!) like the one here (just push the play button!):
I think this is a big step forward for MW. While it is easy to download and install MW, it still removed MW a few clicks from the user and made it "appear to be yet another kind of annoying pop-up" and Charles notes.
It's very easy to do this. The screencast below shows how I made the simulation above in MW. Note that it literally takes one minute (and 5 seconds).
When you hit save you get two files: md.cml and md$0.mml. I transferred these to my web server where I had also put the MW applet (mwapplet.jar).
The html code is
<applet code="org.concord.modeler.MwApplet" archive="mwapplet.jar" height="300" width="100%"><param name="script" value="page:0:import md.cml"></applet>
To include it in a blog, where mwapplet.jar is not installed, add the server address in front of mwapplet.jar and md.cml, e.g. http://myserver.edu/md.cml.

Here is an example of how computational chemistry can be used to enhance teaching at the general chemistry level.

Why does the ionization energy decrease on from Li to Na to K? That's the same as asking why the electron affinities decrease on going from Li+ to Na+ to K+.

Figure 4.2 show the ions colored by how positive they are at the surface (i.e. the electrostatic potential superimposed on the 0.002 isodensity surface). The darker the
color the more positive the ion, and it is clear that the Li+ ion is “more positive” than Na+, which is more positive than K+. Thus, more energy should be released when adding an electron to Li+ compared to Na+, and hence more energy is needed to remove an electron from Li
compared to Na (and similarly for K).

The reason why Li+ is “more positive” than Na+ or, more accurately, why the potential on the 0.002 au isodensity surface is more positive for Li+ than for Na+, is that the former is a smaller ion than the latter, so the surface is closer to the +1 charge at the center of the ion.

This rationalization is, of course, only qualitative and is is not predictive of the ionization energies among different groups. For example, based on Figure 4.4 one would expect that Ne would have roughly the same ionization potential as Na, which is not true at all.

When making these figures it is very important to get the relative sizes of the ions correct, but this can be difficult since each image can be zoomed to an arbitrary size. The screencast below shows how to control this in MacMolPlt using the Manual Windows Parameter window.

The same point can also be made with a "quick-and-dirty" electrostatic potential, as shown in this interactive figure. Here the electrostatic potential is due to a plus one charge centered at the atom (rather than the nuclear charge and the electron density) and the surfaces are the spheres defined by empirical ionic radii. The Jmol script can be found here, and the mol2 files here, here, and here.